Glenn J. Martyna

Chemical doping of large-area stacked graphene films for use as transparent, conducting electrodes

Graphene is considered a leading candidate to replace conventional transparent conducting electrodes because of its high transparency and exceptional transport properties. The effect of chemical p-type doping on graphene stacks was studied in order to reduce the sheet resistance of graphene films to values approaching those of conventional transparent conducting oxides. In this report, we show that large-area, stacked graphene films are effectively p-doped with nitric acid. The doping decreases the sheet resistance by a factor of 3, yielding films comprising eight stacked layers with a sheet resistance of 90 Omega/(square) at a transmittance of 80%. The films were doped either after all of the layers were stacked (last-layer-doped) or after each layer was added (interlayer-doped). A theoretical model that accurately describes the stacked graphene film system as a resistor network was developed. The model defines a characteristic transfer length where all the channels in the graphene films actively contribute to electrical transport. The experimental data shows a linear increase in conductivity with the number of graphene layers, indicating that each layer provides an additional transport channel, in good agreement with the theoretical model.

A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal-isobaric ensemble

The constant-pressure, constant-temperature (NPT) molecular dynamics approach is re-examined from the viewpoint of deriving a new measure-preserving reversible geometric integrator for the equations of motion. The underlying concepts of non-Hamiltonian phase-space analysis, measure-preserving integrators and the symplectic property for Hamiltonian systems are briefly reviewed. In addition, current measure-preserving schemes for the constant-volume, constant-temperature ensemble are also reviewed. A new geometric integrator for the NPT method is presented, is shown to preserve the correct phase-space volume element and is demonstrated to perform well in realistic examples. Finally, a multiple time-step version of the integrator is presented for treating systems with motion on several time scales.

The Role of Chemistry in Graphene Doping for Carbon-Based Electronics

Graphene forms an important two-dimensional (2D) material class that displays both a high electronic conductivity and optical transparency when doped. Yet, the microscopic origin of the doping mechanism in single sheet or bulk intercalated systems remains unclear. Using large-scale ab initio simulations, we show the graphene surface acts as a catalytic reducing/oxidizing agent, driving the chemical disproportionation of adsorbed dopant layers into charge-transfer complexes which inject majority carriers into the 2D carbon lattice. As pertinent examples, we focus on the molecular SbCl(5) and HNO(3) intercalates, and the solid compound AlCl(3). Identifying the microscopic mechanism for the catalytic action of graphene is important, given the availability of large area graphene sheets, to spur research into new redox reactions for use in science and technology.

A new reciprocal space based treatment of long range interactions on surfaces

A new formalism designed to treat long range interactions on surfaces, systems which are infinitely replicated in two spatial directions but have finite extent in the third, is developed. The new formalism is based in reciprocal space and, thus, permits the facile extension of standard plane-wave based density functional theory, Ewald summation, and smooth particle-mesh Ewald methods to handle surfaces efficiently. The method is tested on both model (body centered cubic lattices) and realistic problems (an ice surface with a defect and the 2×1 surface reconstruction of silicon) and found to be accurate, efficient, and a marked improvement on existing formulations in speed, accuracy, and utility.

Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics

In this paper (Paper I) and a companion paper (Paper II), novel new algorithms and applications of the isokinetic ensemble as generated by Gauss’ principle of least constraint, pioneered for use with molecular dynamics 20 years ago, are presented for biophysical, path integral, and Car–Parrinello based ab initio molecular dynamics. In Paper I, a new “extended system” version of the isokinetic equations of motion that overcomes the ergodicity problems inherent in the standard approach, is developed using a new theory of non-Hamiltonian phase space analysis [M. E. Tuckerman et al., Europhys. Lett. 45, 149 (1999); J. Chem. Phys. 115, 1678 (2001)]. Reversible multiple time step integrations schemes for the isokinetic methods, first presented by Zhang [J. Chem. Phys. 106, 6102 (1997)] are reviewed. Next, holonomic constraints are incorporated into the isokinetic methodology for use in fast efficient biomolecular simulation studies. Model and realistic examples are presented in order to evaluate, critically, th...

Fine-grained parallelization of the Car-Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer

Important scientific problems can be treated via ab initio-based molecular modeling approaches, wherein atomic forces are derived from an energy Junction that explicitly considers the electrons. The Car-Parrinello ab initio molecular dynamics (CPAIMD) method is widely used to study small systems containing on the order of 10 to 103 atoms. However, the impact of CPAIMD has been limited until recently because of difficulties inherent to scaling the technique beyond processor numbers about equal to the number of electronic states. CPAIMD computations involve a large number of interdependent phases with high interprocessor communication overhead. These phases require the evaluation of various transforms and non-square matrix multiplications that require large interprocessor data movement when efficiently parallelized. Using the Charm++ parallel programming language and runtime system, the phases are discretized into a large number of virtual processors, which are, in turn, mapped flexibly onto physical processors, thereby allowing interleaving of work. Algorithmic and IBM Blue Gene/L™ system-specific optimizations are employed to scale the CPAIMD method to at least 30 times the number of electronic states in small systems consisting of 24 to 768 atoms (32 to 1,024 electronic states) in order to demonstrate fine-grained parallelism. The largest systems studied scaled well across the entire machine (20,480 nodes).

Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore

Sequencing DNA in a synthetic solid-state nanopore is potentially a low-cost and high-throughput method. Essential to the nanopore-based DNA sequencing method is the ability to control the motion of a single-stranded DNA (ssDNA) molecule at single-base resolution. Experimental studies showed that the average translocation speed of DNA driven by a biasing electric field can be affected by ionic concentration, solvent viscosity, or temperature. Even though it is possible to slow down the average translocation speed, instantaneous motion of DNA is too diffusive to allow each DNA base to stay in front of a sensor site for its measurement. Using extensive all-atom molecular dynamics simulations, we study the diffusion constant, friction coefficient, electrophoretic mobility, and effective charge of ssDNA in a solid-state nanopore. Simulation results show that the spatial fluctuation of ssDNA in 1 ns is comparable to the spacing between neighboring nucleotides in ssDNA, which makes the sensing of a DNA base very difficult. We demonstrate that the recently proposed DNA transistor could potentially solve this problem by electrically trapping ssDNA inside the DNA transistor and ratcheting ssDNA base-by-base in a biasing electric field. When increasing the biasing electric field, we observed that the translocation of ssDNA changes from ratcheting to steady-sliding. The simulated translocation of ssDNA in the DNA transistor was theoretically characterized using Fokker-Planck analysis.

Electrochemical Protection of Thin Film Electrodes in Solid State Nanopores

Solid state nanopores are a core element of next-generation single molecule tools in the field of nano-biotechnology. Thin film electrodes integrated into a pore can interact with charges and fields within the pore. In order to keep the nanopore open and thus functional electrochemically induced surface alteration of electrode surfaces and bubble formation inside the pore have to be eliminated. This paper provides electrochemical analyses of nanopores drilled into TiN membranes which in turn were employed as thin film electrodes. We studied physical pore integrity and the occurrence of water decomposition yielding bubble formation inside pores by applying voltages between -4.5 and +4.5 V to membranes in various protection stages continuously for up to 24 h. During potential application pores were exposed to selected electrolyte-solvent systems. We have investigated and successfully eliminated electrochemical pore oxidation and reduction as well as water decomposition inside nanopores of various diameters ranging from 3.5 to 25 nm in 50 nm thick TiN membranes by passivating the nanopores with a plasma-oxidized layer and using a 90% solution of glycerol in water as KCl solvent. Nanopore ionic conductances were measured before and after voltage application in order to test for changes in pore diameter due to electrochemical oxidation or reduction. TEM imaging was used to confirm these observations. While non-passivated pores were electrochemically oxidized, neither electrochemical oxidation nor reduction was observed for passivated pores. Bubble formation through water decomposition could be detected in non-passivated pores in KCl/water solutions but was not observed in 90% glycerol solutions. The use of a protective self-assembled monolayer of hexadecylphosphonic acid (HDPA) was also investigated.

Carbon nanotube thin film transistors on flexible substrates

Carbon nanotube thin film transistors (CNT-TFTs) are fabricated on flexible substrates using purified, surfactant-based CNT suspensions, with >95% semiconducting CNT fraction. The TFTs are made up of local bottom-gated structures with aluminum oxide as the gate dielectric. The devices exhibit high ON current densities (0.1 μA/μm) and on-off ratios (∼105) with mobility values ranging from 10-35 cm2/Vs. A detailed numerical model is used to understand the TFT performance and its dependence on device parameters such as TFT channel length, CNT density, and purity.

High Response Piezoelectric and Piezoresistive Materials for Fast, Low Voltage Switching: Simulation and Theory of Transduction Physics at the Nanometer‐Scale

Field effect transistors are reaching the limits imposed by the scaling of materials and the electrostatic gating physics underlying the device. In this Communication, a new type of switch based on different physics, which combines known piezoelectric and piezoresistive materials, is described and is shown by theory and simulation to achieve gigahertz digital switching at low voltage (0.1 V).